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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
CDKL5
cyclin dependent kinase like 5
Chromosome X Β· Xp22.13
NCBI Gene: 6792Ensembl: ENSG00000008086.13HGNC: HGNC:11411UniProt: O76039
143PubMed Papers
21Diseases
0Drugs
588Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedKinase
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
kinase activitymodulation of chemical synaptic transmissionnucleoplasmregulation of postsynapse organizationdevelopmental and epileptic encephalopathy, 2CDKL5 disorderAngelman syndromeatypical Rett syndrome
✦AI Summary

CDKL5 is an X-linked serine/threonine kinase critical for early brain development and neuronal function. Mechanistically, CDKL5 mediates phosphorylation of MECP2 12 and regulates essential processes including axon outgrowth, dendritic morphogenesis, synapse formation and maintenance 3. The gene may also regulate ciliogenesis through ciliary basal body and centrosome functions. CDKL5 deficiency disorder (CDD) is a rare developmental and epileptic encephalopathy characterized by early-onset seizures (typically within the first 2 months of life) that are usually refractory to conventional antiseizure medications 4. Affected individuals experience severely impaired development, with only 25% of girls achieving independent walking, alongside gastrointestinal, sleep, and musculoskeletal complications 4. CDD is classified as an X-linked developmental epileptic encephalopathy 5. Clinically, early genetic diagnosis is essential to provide appropriate family counseling and management strategies. Current therapeutic options including ketogenic diets and vagal nerve stimulation provide limited benefit, though gene replacement therapy using AAV9-mediated CDKL5 delivery shows promise in preclinical studies, with functional improvements observed in knockout mice at sufficient transfection levels 3. Disease-modifying therapies represent emerging treatment directions.

Sources cited
1
CDKL5 mediates phosphorylation of MECP2
PMID: 15917271
2
CDKL5 mediates phosphorylation of MECP2
PMID: 16935860
3
CDKL5 is a serine/threonine kinase critical for axon outgrowth, dendritic morphogenesis, and synapse formation/maintenance; gene replacement therapy proof of concept
PMID: 39033321
4
CDKL5 deficiency disorder characterized by early-onset refractory seizures within first 2 months, severe developmental impairment, gastrointestinal/sleep/musculoskeletal complications, limited benefit from conventional treatments
PMID: 35483386
5
CDKL5-related DEE is classified as an X-linked developmental and epileptic encephalopathy
PMID: 38612920
Disease Associationsβ“˜21
developmental and epileptic encephalopathy, 2Open Targets
0.85Strong
CDKL5 disorderOpen Targets
0.72Strong
Angelman syndromeOpen Targets
0.67Moderate
atypical Rett syndromeOpen Targets
0.64Moderate
X-linked retinoschisisOpen Targets
0.59Moderate
infantile spasmsOpen Targets
0.58Moderate
Retinal dystrophyOpen Targets
0.57Moderate
genetic disorderOpen Targets
0.55Moderate
Rett syndromeOpen Targets
0.54Moderate
Epileptic encephalopathyOpen Targets
0.51Moderate
retinoschisisOpen Targets
0.51Moderate
SeizureOpen Targets
0.49Moderate
early-infantile DEEOpen Targets
0.46Moderate
developmental and epileptic encephalopathyOpen Targets
0.43Moderate
autismOpen Targets
0.41Moderate
Intellectual disabilityOpen Targets
0.37Weak
Global developmental delayOpen Targets
0.34Weak
partial epilepsyOpen Targets
0.34Weak
stereotypic movement disorderOpen Targets
0.34Weak
Stereotypical hand wringingOpen Targets
0.34Weak
Developmental and epileptic encephalopathy 2UniProt
Pathogenic Variants588
NM_001323289.2(CDKL5):c.351T>A (p.Tyr117Ter)Pathogenic
not provided|CDKL5 disorder
β˜…β˜…β˜…β˜†2025β†’ Residue 117
NM_001323289.2(CDKL5):c.863C>G (p.Thr288Arg)Likely pathogenic
not provided|Developmental and epileptic encephalopathy, 2;Angelman syndrome-like|CDKL5 disorder
β˜…β˜…β˜…β˜†2025β†’ Residue 288
NM_001323289.2(CDKL5):c.578A>T (p.Asp193Val)Likely pathogenic
Developmental and epileptic encephalopathy, 2;Angelman syndrome-like|CDKL5 disorder
β˜…β˜…β˜…β˜†2025β†’ Residue 193
NM_001323289.2(CDKL5):c.656A>C (p.Gln219Pro)Likely pathogenic
Atypical Rett syndrome|Inborn genetic diseases|CDKL5 disorder
β˜…β˜…β˜…β˜†2025β†’ Residue 219
NM_001323289.2(CDKL5):c.372_385del (p.His124fs)Pathogenic
Angelman syndrome-like;Developmental and epileptic encephalopathy, 2|CDKL5 disorder
β˜…β˜…β˜…β˜†2025β†’ Residue 124
NM_001323289.2(CDKL5):c.545T>C (p.Leu182Pro)Likely pathogenic
CDKL5 disorder|not provided
β˜…β˜…β˜…β˜†2025β†’ Residue 182
NM_001323289.2(CDKL5):c.38T>C (p.Phe13Ser)Likely pathogenic
Developmental and epileptic encephalopathy, 2|Developmental and epileptic encephalopathy, 2;Angelman syndrome-like|CDKL5 disorder
β˜…β˜…β˜…β˜†2025β†’ Residue 13
NM_001323289.2(CDKL5):c.220G>T (p.Glu74Ter)Pathogenic
not provided|CDKL5 disorder
β˜…β˜…β˜…β˜†2025β†’ Residue 74
NM_001323289.2(CDKL5):c.2152G>A (p.Val718Met)Pathogenic
not provided|Developmental and epileptic encephalopathy, 2|CDKL5 disorder
β˜…β˜…β˜…β˜†2025β†’ Residue 718
NM_001323289.2(CDKL5):c.2500C>T (p.Gln834Ter)Pathogenic
Developmental and epileptic encephalopathy, 2|Atypical Rett syndrome|Developmental and epileptic encephalopathy, 2;Angelman syndrome-like|CDKL5 disorder
β˜…β˜…β˜…β˜†2024β†’ Residue 834
NM_001323289.2(CDKL5):c.146-1G>APathogenic
Developmental and epileptic encephalopathy, 2|not provided|CDKL5 disorder
β˜…β˜…β˜…β˜†2024
NM_001323289.2(CDKL5):c.1311dup (p.Ser438fs)Pathogenic
Atypical Rett syndrome|CDKL5 disorder
β˜…β˜…β˜…β˜†2024β†’ Residue 438
NM_001323289.2(CDKL5):c.469G>C (p.Ala157Pro)Likely pathogenic
Angelman syndrome-like;Developmental and epileptic encephalopathy, 2|CDKL5 disorder
β˜…β˜…β˜…β˜†2023β†’ Residue 157
NM_001323289.2(CDKL5):c.290T>C (p.Leu97Pro)Likely pathogenic
Developmental and epileptic encephalopathy, 2|Angelman syndrome-like;Developmental and epileptic encephalopathy, 2|CDKL5 disorder
β˜…β˜…β˜…β˜†2023β†’ Residue 97
NM_001323289.2(CDKL5):c.65G>A (p.Gly22Glu)Likely pathogenic
Developmental and epileptic encephalopathy, 2|Developmental and epileptic encephalopathy, 2;Angelman syndrome-like|CDKL5 disorder|Thyroid cancer, nonmedullary, 1
β˜…β˜…β˜…β˜†2023β†’ Residue 22
NM_001323289.2(CDKL5):c.454T>C (p.Cys152Arg)Likely pathogenic
Developmental and epileptic encephalopathy, 2;Angelman syndrome-like|Developmental and epileptic encephalopathy, 2|CDKL5 disorder
β˜…β˜…β˜…β˜†2023β†’ Residue 152
NM_001323289.2(CDKL5):c.2151A>G (p.Arg717=)Likely pathogenic
not provided|Developmental and epileptic encephalopathy, 2;Angelman syndrome-like|CDKL5 disorder|Nonpapillary renal cell carcinoma
β˜…β˜…β˜…β˜†2023β†’ Residue 717
NM_001323289.2(CDKL5):c.470C>T (p.Ala157Val)Likely pathogenic
not specified|not provided|Angelman syndrome-like;Developmental and epileptic encephalopathy, 2|Developmental and epileptic encephalopathy, 2|CDKL5 disorder
β˜…β˜…β˜…β˜†2023β†’ Residue 157
NM_001323289.2(CDKL5):c.2842C>T (p.Arg948Ter)Pathogenic
not provided|Developmental and epileptic encephalopathy, 2|CDKL5 disorder|Developmental and epileptic encephalopathy
β˜…β˜…β˜…β˜†2022β†’ Residue 948
NM_001323289.2(CDKL5):c.2821del (p.Tyr941fs)Pathogenic
Developmental and epileptic encephalopathy, 2;Angelman syndrome-like|not provided|CDKL5 disorder|Developmental and epileptic encephalopathy, 2
β˜…β˜…β˜…β˜†2022β†’ Residue 941
View on ClinVar β†—
Related Genes
PCDH19Protein interaction94%UBE3AProtein interaction87%FOXG1Protein interaction87%MECP2Protein interaction87%STXBP1Protein interaction85%NTNG1Protein interaction85%
Tissue Expression6 tissues
Brain
100%
Lung
46%
Heart
38%
Ovary
34%
Bone Marrow
16%
Liver
13%
Gene Interaction Network
Click a node to explore
CDKL5PCDH19UBE3AFOXG1MECP2STXBP1NTNG1
PROTEIN STRUCTURE
Preparing viewer…
PDB4BGQ Β· 2.00 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.23Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.13 [0.08–0.23]
RankingsWhere CDKL5 stands among ~20K protein-coding genes
  • #3,189of 20,598
    Most Researched143 Β· top quartile
  • #83of 5,498
    Most Pathogenic Variants588 Β· top 5%
  • #653of 17,882
    Most Constrained (LOEUF)0.23 Β· top 5%
Genes detectedCDKL5
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
International consensus on diagnosis and management of Dravet syndrome.
PMID: 35490361
Epilepsia Β· 2022
1.00
2
Genetic therapeutic advancements for Dravet Syndrome.
PMID: 35653814
Epilepsy Behav Β· 2022
0.90
3
CDKL5 deficiency disorder: clinical features, diagnosis, and management.
PMID: 35483386
Lancet Neurol Β· 2022
0.80
4
X-Linked Epilepsies: A Narrative Review.
PMID: 38612920
Int J Mol Sci Β· 2024
0.70
5
Preclinical studies of gene replacement therapy for CDKL5 deficiency disorder.
PMID: 39033321
Mol Ther Β· 2024
0.60